Abstract
One of the most important challenges in agriculture is to determine the effectiveness and environmental impact of certain farming practices. The aim of present study was to determine and compare the taxonomic composition of the microbiomes established in soil following long-term exposure (14 years) to a conventional and organic farming systems (CFS and OFS accordingly). Soil from unclared forest next to the fields was used as a control. The analysis was based on RT-PCR and pyrosequencing of 16S rRNA genes of bacteria and archaea. The number of bacteria was significantly lower in CFS than in OFS and woodland. The highest amount of archaea was detected in woodland, whereas the amounts in CFS and OFS were lower and similar. The most common phyla in the soil microbial communities analyzed were Proteobacteria (57.9%), Acidobacteria (16.1%), Actinobacteria (7.9%), Verrucomicrobia (2.0%), Bacteroidetes (2.7%) and Firmicutes (4.8%). Woodland soil differed from croplands in the taxonomic composition of microbial phyla. Croplands were enriched with Proteobacteria (mainly the genus Pseudomonas), while Acidobacteria were detected almost exclusively in woodland soil. The most pronounced differences between the CFS and OFS microbiomes were found within the genus Pseudomonas, which significantly (p<0,05) increased its number in CFS soil compared to OFS. Other differences in microbiomes of cropping systems concerned minor taxa. A higher relative abundance of bacteria belonging to the families Oxalobacteriaceae, Koribacteriaceae, Nakamurellaceae and genera Ralstonia, Paenibacillus and Pedobacter was found in CFS as compared with OFS. On the other hand, microbiomes of OFS were enriched with proteobacteria of the family Comamonadaceae (genera Hylemonella) and Hyphomicrobiaceae, actinobacteria from the family Micrococcaceae, and bacteria of the genera Geobacter, Methylotenera, Rhizobium (mainly Rhizobium leguminosarum) and Clostridium. Thus, the fields under OFS and CFS did not differ greatly for the composition of the microbiome. These results, which were also confirmed by cluster analysis, indicated that microbial communities in the field soil do not necessarily differ largely between conventional and organic farming systems.
Highlights
Soil microorganisms can serve as bioindicators of anthropogenic stress experienced by the soil during agricultural use [1]
Relative quantities of bacteria and archaea estimated by quantitative PCR (qPCR)
The copy number of ribosomal operons in the genomes of microorganisms varies and is, in average, 4.09 for bacteria and 1.76 for archaea according to the rrnDB database [36]
Summary
Soil microorganisms can serve as bioindicators of anthropogenic stress experienced by the soil during agricultural use [1]. For a long period of time, biologically valuable soil microorganisms have been studied by isolation and cultivation in laboratory [2]. The next-generation sequencing technologies have intensified exploration of soil microbial diversity and allowed to identify biological indicators, among the microbes that can be cultured in vitro, and among the bacteria and archaea which cannot be cultured [3]. One of the most important challenges of modern agriculture is to determine the effectiveness and environmental impact of systems based on organic or conventional farming (OFS and CFS respectively). Productivity in CFS is generally higher than in OFS, but the negative impact on the environment associated with the use of a particular type of farming system is debated [7,8,9]
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